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The data base, and some
Thanks to ...
A Data Base of PCR Primers for the Study of the Chloroplast
Genome in Plants
Berthold Heinze Federal Forest Research Centre -
Institute of Forest Genetics, Vienna, AUSTRIA
Version 1.0 (November 2002 - 356 primer sequences)
- Heinze B. , 2001:
A data base
for PCR primers in the chloroplast genome. Poster presented at Plant and
Animal Genome X, Jan 12-16, 2002, San Diego, CA, USA.
http://bfw.ac.at/200/1859.html (this document)
- Heinze, B.; Grivet, D.; Petit, R.; Hahn, B , 1999: A
comprehensive set of PCR primers for the study of the chloroplast genome in
plants. "Networking Day Genomics" (BIT and BMBWK), Wien, Mai 1999. Poster
- Heinze, B. , 1999:
chloroplast DNA investigations in some hardwood forest trees using PCR-RFLP
analysis. Plant and Animal Genome VII, Jan. 17-21, , San Diego, USA ,
have described the use of "universal" primers for PCR from chloroplast DNA,
i.e., primers that amplify DNA fragments from many species in a genus, family,
or even higher taxonomic groupings (see dedicated list of references). Usually,
such primers are based on conserved DNA sequence in exons. The information is
contained in a few comprehensive articles and many scattered primer sequences
in other publications.
For use in molecular population genetics and taxonomy, large
numbers of markers are necessary. Their (known) levels of polymorphism should
fit diverse applications. They should be applicable for many species, and lend
temselves to rapid screening methods.
However, marker development for such 'universal PCR' is
time-consuming, so markers that can be transferred between species are
desirable. This is possible with 'classical' RFLP probes. As shown by several
authors, it is also possible with PCR primers, but to what extent ? The
database compiled here will provide a starting ground to estimate primer
'universality'. In chloroplast spacers, gene order is highly conserved, and
spacers show intra-species variation. Small indels predominate. Exon sequences
are generally highly conserved, but this depends on the gene in question.
Some problems with universal PCR include the more rapid
sequence evolution in some parts of the chloroplast; the identification of
polymorphisms between conserved primer sites (introns); and occasional
rearrangements, deletions, duplications in some genera, families, or higher
Sets of dedicated 'universal' chloroplast primers for
amplifying spacers and introns have been described by Taberlet et al. 1991,
Demesure et al. 1995, Dumolin-Lapegue et al. 1997, Fofana et al. 1997, Hamilton
1999, and Grivet et al. 2001. In the latter publication, the large single copy
region of the chloroplast ring is covered by 38 primer pairs. Amplified
fragments can be analysed by restriction or sequencing.
'Universal' chloroplast primers have also been developed for
comparative sequencing in phylogeny, e.g. in the rbcL gene, for obtaining
phylogenies of land plants. Other genes with different mutation rates can
resolve certain problems, e.g. matK, ndhF, rpl16, and atpB.